# HG changeset patch
# User bgruening
# Date 1550565937 18000
# Node ID 231b4f3228cc20de726bd317f7ca792f730b9f23
# Parent  708beeae12958089e07a99b95b3d0e867dc99bb6
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d

diff -r 708beeae1295 -r 231b4f3228cc bamCompare.xml
--- a/bamCompare.xml	Tue Aug 21 16:57:19 2018 -0400
+++ b/bamCompare.xml	Tue Feb 19 03:45:37 2019 -0500
@@ -63,6 +63,7 @@
 
                 @ADVANCED_OPTS_READ_PROCESSING@
                 $advancedOpt.skipNAs
+                $advancedOpt.skipZeroOverZero
 
                 #if str($advancedOpt.ignoreForNormalization).strip() != '':
                     --ignoreForNormalization '$advancedOpt.ignoreForNormalization'
@@ -163,6 +164,11 @@
                 <expand macro="read_processing_options" />
 
                 <expand macro="skipNAs" />
+                <param argument="--skipZeroOverZero" type="select" label="Skip bins of no coverage"
+                    help="Skip bins where BOTH files lack coverage.">
+                    <option value="no" selected="true">No</option>
+                    <option value="yes">Yes, skip them.</option>
+                </param>
 
                 <param argument="--ignoreForNormalization" type="text" value="" size="50"
                     label="regions that should be excluded for calculating the scaling factor"
diff -r 708beeae1295 -r 231b4f3228cc deepTools_macros.xml
--- a/deepTools_macros.xml	Tue Aug 21 16:57:19 2018 -0400
+++ b/deepTools_macros.xml	Tue Feb 19 03:45:37 2019 -0500
@@ -1,11 +1,11 @@
 <macros>
 
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">3.1.2.0</token>
+    <token name="@WRAPPER_VERSION@">3.2.0.0</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="3.1.2">deeptools</requirement>
-            <requirement type="package" version="1.7">samtools</requirement>
+            <requirement type="package" version="3.2.0">deeptools</requirement>
+            <requirement type="package" version="1.9">samtools</requirement>
         </requirements>
         <expand macro="stdio" />
         <version_command>@BINARY@ --version</version_command>
@@ -359,7 +359,7 @@
     </xml>
 
     <xml name="pseudocount">
-        <param argument="--pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
+        <param argument="--pseudocount" type="text" value="1 1" label="Pseudocount" help="Small number to avoid dividing by zero. You can specify separate values for the pseudocount added to the numerator and denominator by providing two values separated by a space."/>
     </xml>
 
     <token name="@REFERENCES@">
@@ -423,12 +423,47 @@
         </conditional>
     </xml>
 
+    <xml name="custom_sample_labels">
+	<conditional name="custom_sample_labels_conditional">
+        <param name="custom_labels_select" type="select" label="Would you like custom sample labels?" help="By default, the names of the samples in your history are used.">
+	    <option value="No" selected="true">No, use sample names in the history</option>
+	    <option value="Yes">Yes, I want to specify new labels</option>
+	</param>
+	<when value="No">
+	</when>
+	<when value="Yes">
+	    <param argument="--labels" type="text" label="Sample Labels" help="Labels, separated by a space. If your labels themselves contain spaces then please enclose them in quotes (e.g., &quot;sample 1&quot; &quot;sample 2&quot;)">
+                <sanitizer>
+                    <valid initial="string.printable">
+                    </valid>
+                </sanitizer>
+            </param>
+	</when>
+        </conditional>
+    </xml>
+
     <xml name="plotTitle">
         <param argument="--plotTitle" type="text" value="" size="30" optional="True"
             label="Title of the plot"
             help="Title of the plot, to be printed on top of the generated image." />
     </xml>
 
+    <xml name="legendLocation">
+        <param argument="--legendLocation" type="select" label="Legend location" help="Location for the legend in the summary plot. Note that none cannot be used in plotProfile.">
+            <option value="best" selected="true">Best (automatic)</option>
+            <option value="upper-right">upper-right</option>
+            <option value="upper-left">upper-left</option>
+            <option value="upper-center">upper-center</option>
+            <option value="lower-right">lower-right</option>
+            <option value="lower-left">lower-left</option>
+            <option value="lower-center">lower-center</option>
+            <option value="center-right">center-right</option>
+            <option value="center-left">center-left</option>
+            <option value="center">center</option>
+            <option value="none">none (only works for heatmaps</option>
+        </param>
+    </xml>
+
     <xml name="labelRotation">
         <param argument="--labelRotation" type="integer" value="0"
             label="Rotation of the X-axis labels (in degrees)"
@@ -438,6 +473,9 @@
 
     <token name="@multiple_input_bams@">
 <![CDATA[
+        #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
+            #set custom_labels=labels
+        #end if
         #set files=[]
         #set labels=[]
         #import re
@@ -466,11 +504,17 @@
                 #silent $labels.append("'%s'" % $identifier)
             #end for
         #end if
+        #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
+            #set labels=custom_labels
+        #end if
 ]]>
     </token>
 
     <token name="@multiple_input_bigwigs@">
 <![CDATA[
+        #if $custom_labels_conditional.custom_labels_select == "Yes":
+            #set custom_labels=labels
+        #end if
         #set files=[]
         #set labels=[]
         #import re
@@ -489,6 +533,9 @@
                 #silent $labels.append("'%s'" % $identifier)
             #end for
         #end if
+        #if $custom_labels_conditional.custom_labels_select == "Yes":
+            #set labels=custom_labels
+        #end if
 ]]>
     </token>
 
diff -r 708beeae1295 -r 231b4f3228cc repository_dependencies.xml
--- a/repository_dependencies.xml	Tue Aug 21 16:57:19 2018 -0400
+++ b/repository_dependencies.xml	Tue Feb 19 03:45:37 2019 -0500
@@ -1,4 +1,4 @@
-<?xml version="1.0"?>
+<?xml version="1.0" ?>
 <repositories>
-    <repository changeset_revision="fced964b054a" name="data_manager_twobit_builder" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-</repositories>
+    <repository changeset_revision="fced964b054a" name="data_manager_twobit_builder" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu"/>
+</repositories>
\ No newline at end of file